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Research: Comprehensive isoform-level analysis reveals the contribution of alternative isoforms to venom evolution and repertoire diversity
- Xinhai Ye,
- Chun He,
- Yi Yang,
- Yu H. Sun,
- Shijiao Xiong,
- Kevin C. Chan,
- Yuxuan Si,
- Shan Xiao,
- Xianxin Zhao,
- Haiwei Lin,
- Yang Mei,
- Yufeng Yao,
- Gongyin Ye,
- Fei Wu,
- and Qi Fang
Genome Res. September 2023 33: 1554-1567; Published in Advance October 5, 2023, doi:10.1101/gr.277707.123
...isoform profiling workflow based on long-read sequencing. Our focus was on Pteromalus puparum, a representative parasitoid wasp species with a global distribution. By analyzing the isoform landscape of venom genes, along with gene/isoform expression and venom proteome data, we aimed to elucidate the role...
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Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
- Kamal Ajit,
- Adele Alagia,
- Kaspar Burger,
- and Monika Gullerova
Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
...Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage Kamal Ajit1, Adele Alagia1, Kaspar Burger2,3 and Monika Gullerova1 1Sir William Dunn School of Pathology, Oxford, OX1 3RE...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...of each genomic locus to all other genomic loci by integrating k-step (k = 1, 2, 3, ……) transition probability matrices derived from a Hi-C contact matrix (see Methods). Taking all other genomic loci into consideration, the diffusion property is hence defined based on global information of the Hi...
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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
...and silencing-complex maturation. Within Argonaute, guide strands have stabilities that vary by 100-fold. Half-lives also vary globally between cell lines, with median values ranging from 11 to 34 h in mESCs and contact-inhibited MEFs, respectively. Moreover, relative half-lives for individual miRNAs vary...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
..., there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. By using translating ribosome affinity purification coupled with deep-sequencing (TRAP-seq) in Caenorhabditis elegans, we have obtained high coverage...
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Research: Long-read sequencing of nascent RNA reveals coupling among RNA processing events
- Lydia Herzel,
- Korinna Straube,
- and Karla M. Neugebauer
Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
...(Wahl et al. 2009). Global short-read sequencing (RNA-seq) of nascent RNA from yeast to human has revealed that most introns are removed from pre-mRNA during transcription by RNA polymerase II (Pol II) (Brugiolo et al. 2013). Therefore, spliceosome assembly and splicing occur on nascent RNA...
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Method: Control of fluxes in metabolic networks
- Georg Basler,
- Zoran Nikoloski,
- Abdelhalim Larhlimi,
- Albert-László Barabási,
- and Yang-Yu Liu
Genome Res. July 2016 26: 956-968; Published in Advance May 19, 2016, doi:10.1101/gr.202648.115
...(cluster 4). Moreover, the cancer networks (clusters 2 and 4) are clearly separated from the corresponding healthy tissues (cluster 5), suggesting that distinct coupling patterns characterize healthy and cancer tissues. In particular, the flux coupling profiles of all nine considered eukaryotes form...
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Resource: A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation
- Andreas J. Gruber,
- Ralf Schmidt,
- Andreas R. Gruber,
- Georges Martin,
- Souvik Ghosh,
- Manuel Belmadani,
- Walter Keller,
- and Mihaela Zavolan
Genome Res. August 2016 26: 1145-1159; Published in Advance July 5, 2016, doi:10.1101/gr.202432.115
...partially. For example, the core 3′ end processing factor FIP1L1 can bind poly(U) (Kaufmann et al. 2004; Lackford et al. 2014), and its knock-down causes a systematic increase in 3′ UTR lengths (Lackford et al. 2014; Li et al. 2015). HNRNPC knock-down causes global changes in alternative cleavage...
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Research: Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks
- Endre Sebestyén,
- Babita Singh,
- Belén Miñana,
- Amadís Pagès,
- Francesca Mateo,
- Miguel Angel Pujana,
- Juan Valcárcel,
- and Eduardo Eyras
Genome Res. June 2016 26: 732-744; Published in Advance April 13, 2016, doi:10.1101/gr.199935.115
...to be comprehensively described. To elucidate the complete set of alterations in these factors and how they globally affect alternative splicing that may contribute to cancer, we analyzed RNA and DNA sequencing data from The Cancer Genome Atlas (TCGA) project for 11 solid tumor types.ResultsRBPs are frequently de...
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LETTER: Three distinct modes of intron dynamics in the evolution of eukaryotes
- Liran Carmel,
- Yuri I. Wolf,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. July 2007 17: 1034-1044; Published in Advance May 10, 2007, doi:10.1101/gr.6438607
..., such global counting is not particularly illuminating as lineages vastly differ in their gain and loss patterns, and, furthermore, these patterns are hardly uniform in time. In the following, we analyze the comparative contributions of intron gains and losses in different parts of the eukaryotic tree and...
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